Sir Peter MacCallum Department of Oncology - Research Publications

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Author: Devereux, Lisa × Author: Fox, Stephen × Author: Gorringe, Kylie × End date: 2019 × Start date: 2015 ×

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    Molecular comparison of interval and screen-detected breast cancers
    Cheasley, D ; Li, N ; Rowley, SM ; Elder, K ; Mann, GB ; Loi, S ; Savas, P ; Goode, DL ; Kader, T ; Zethoven, M ; Semple, T ; Fox, SB ; Pang, J-M ; Byrne, D ; Devereux, L ; Nickson, C ; Procopio, P ; Lee, G ; Hughes, S ; Saunders, H ; Fujihara, KM ; Kuykhoven, K ; Connaughton, J ; James, PA ; Gorringe, KL ; Campbell, IG (WILEY, 2019-06)
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    Reevaluation of the BRCA2 truncating allele c.9976A > T (p.Lys3326Ter) in a familial breast cancer context
    Thompson, ER ; Gorringe, KL ; Rowley, SM ; Li, N ; McInerny, S ; Wong-Brown, MW ; Devereux, L ; Li, J ; Trainer, AH ; Mitchell, G ; Scott, RJ ; James, PA ; Campbell, IG (NATURE PORTFOLIO, 2015-10-12)
    The breast cancer predisposition gene, BRCA2, has a large number of genetic variants of unknown effect. The variant rs11571833, an A > T transversion in the final exon of the gene that leads to the creation of a stop codon 93 amino acids early (K3326*), is reported as a neutral polymorphism but there is some evidence to suggest an association with an increased risk of breast cancer. We assessed whether this variant was enriched in a cohort of breast cancer cases ascertained through familial cancer clinics compared to population-based non-cancer controls using a targeted sequencing approach. We identified the variant in 66/2634 (2.5%) cases and 33/1996 (1.65%) controls, indicating an enrichment in the breast cancer cases (p = 0.047, OR 1.53, 95% CI 1.00-2.34). This data is consistent with recent iCOGs data suggesting that this variant is not neutral with respect to breast cancer risk. rs11571833 may need to be included in SNP panels for evaluating breast cancer risk.
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    Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue
    Kader, T ; Goode, DL ; Wong, SQ ; Connaughton, J ; Rowley, SM ; Devereux, L ; Byrne, D ; Fox, SB ; Arnau, GM ; Tothill, RW ; Campbell, IG ; Gorringe, KL (BMC, 2016-11-15)
    Unlocking clinically translatable genomic information, including copy number alterations (CNA), from formalin-fixed paraffin-embedded (FFPE) tissue is challenging due to low yields and degraded DNA. We describe a robust, cost-effective low-coverage whole genome sequencing (LC WGS) method for CNA detection using 5 ng of FFPE-derived DNA. CN profiles using 100 ng or 5 ng input DNA were highly concordant and comparable with molecular inversion probe (MIP) array profiles. LC WGS improved CN profiles of samples that performed poorly using MIP arrays. Our technique enables identification of driver and prognostic CNAs in archival patient samples previously deemed unsuitable for genomic analysis due to DNA limitations.